Dear SfePy Users,
I want to solve a thermal problem with the following issues
- several separated regions (bodies) that
- exchange heat via radiation and
- have anisotropic, temperature dependend material properties.
The core of this problem is that the boundary conditions (heat flux given by radiation) are non-local, i.e. they depend on the dependent variable (temperature) of other boundary regions.
Can I solve this kind of problem with SfePy?
Thanks for input
Michael
Thanks
Michael
I am pleased to announce release 2020.1 of SfePy.
Description
-----------
SfePy (simple finite elements in Python) is a software for solving systems of
coupled partial differential equations by the finite element method or by the
isogeometric analysis (limited support). It is distributed under the new BSD
license.
Home page: http://sfepy.org
Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/
Git (source) repository, issue tracker: https://github.com/sfepy/sfepy
Highlights of this release
--------------------------
- reading/writing of additional mesh formats by using meshio [2]
- Python 3 only from now on
For full release notes see [1].
Cheers,
Robert Cimrman
[1] http://docs.sfepy.org/doc/release_notes.html#id1
[2] https://github.com/nschloe/meshio
---
Contributors to this release in alphabetical order:
Robert Cimrman
Lubos Kejzlar
Vladimir Lukes
The latest commits in the master branch on github incorporate meshio
package [1] into SfePy. We use meshio to read the following file
formats: abaqus, exodus, gmsh, medit, nastran, vtk, vtu, med, xdmf and
tetgen. Besides these formats, we keep on maintaining own code for
reading: ansys_cdb, xyz, comsol, hmascii, gambit and mesh3d.
Bug fixes and improvements are welcome!
Regards,
Vladimír Lukeš
[1] https://github.com/nschloe/meshio
I want to define my own field. For example, pressure.
```python
fields = {
'temperature' : ('real', 1, 'Omega', 1),
'pressure' : ('real', 1, 'Omega', 1),
}
variables = {
't' : ('unknown field', 'temperature', 0),
's' : ('test field', 'temperature', 't'),
'p' : ( 'parameter field', 'pressure', {'setter' : 'get_pressure'} ),
}
def get_pressure(ts, coors, region=None):
z = coors[:,2]
return z
functions = {
'get_pressure': (get_pressure,),
}
```
The idea is to create very primitive field that depends on z coordinates.
Now I want to export the grad(p) to the output mesh. And so I add this in
postprocess function:
```python
p_grad = pb.evaluate('ev_grad.i.Omega(p)', mode='el_avg', verbose=False)
out['p'] = Struct(name='output_data', mode='cell', data=p_grad, dofs=None)
```
But I get the following error:
ValueError: argument p not found!
What I'm doing wrong?
And how can I export the pressure field itself (not its gradient)?
The answer from Robert Cimrman:
Hi,
In a post-processing function, the only variables that are defined are
those
that are used in the equations. If p is not used, you need to create it, as
shown below (also how to save p and its cell averages.
def post_process(out, pb, state, extend=False):
from sfepy.base.base import Struct
pvar = pb.create_variables(['p'])['p']
pvar.time_update(None, pb.functions)
out.update(pvar.create_output())
ap = pb.evaluate('ev_volume_integrate.i.Omega(p)', mode='el_avg',
p=pvar,
verbose=False)
out['ap'] = Struct(name='output_data', mode='cell', data=ap, dofs=None)
p_grad = pb.evaluate('ev_grad.i.Omega(p)', mode='el_avg', p=pvar,
verbose=False)
out['gp'] = Struct(name='output_data', mode='cell', data=p_grad,
dofs=None)
return out
r.
PS: This might be interesting to others, so, if you do not mind, you can
forward it to the list.
Yes, mmesh.point_data['mat_ids'] would work, but I did not see it in your mesh :)
r.
On 2/3/20 4:43 AM, FaTune wrote:
> Your little snipped has worked like magic! Thank you so much!
>
> Am I right that to also save 'mat_ids' I have to change the argument
> [np.zeros_like(conn[:, 0])] to mmesh.point_data['mat_ids']?
>
> ```python
> smesh = Mesh.from_data(
> 'meshio-mesh',
> mmesh.points,
> mmesh.point_data['node_groups'],
> [conn],
> mmesh.point_data['mat_ids'],
> ['3_4'],
> )
> ```
>
> On Mon, Feb 3, 2020 at 3:45 AM Robert Cimrman <cimrman3(a)ntc.zcu.cz> wrote:
>
>> I was thinking about meshio too. But because it does not write the old VTK
>> format, you could try the following:
>>
>> ```
>> import numpy as np
>> import meshio
>>
>> from sfepy.discrete.fem import Mesh
>>
>> mmesh = meshio.read('trian.vtk')
>>
>> conn = mmesh.cells['tetra']
>> smesh = Mesh.from_data(
>> 'meshio-mesh',
>> mmesh.points,
>> mmesh.point_data['node_groups'],
>> [conn],
>> [np.zeros_like(conn[:, 0])],
>> ['3_4'],
>> )
>>
>> smesh.write('trian2.vtk')
>> ```
>>
>> Then
>>
>> postproc.py --only-names=node_groups -b trian2.vtk --wire
>>
>> seems to show the regions correctly.
>>
>> r.
>>
>> On 2/2/20 1:14 PM, FaTune wrote:
>>> Thank you for help. I'm not sure I know how to convert the mesh into
>> older
>>> format. Is there any converter? I've tried to convert trian.vtk to
>>> trian.mesh using meshio-convert in ubuntu. But the resulting trian.mesh
>>> doesn't have any information about node_groups.
>>>
>>> On Sun, Feb 2, 2020 at 9:05 PM Robert Cimrman <cimrman3(a)ntc.zcu.cz>
>> wrote:
>>>
>>>> Can you try converting the mesh to "# vtk DataFile Version 2.0" format?
>>>> Your
>>>> mesh is in "# vtk DataFile Version 4.2", and the reader in sfepy does
>> not
>>>> read
>>>> it correctly.
>>>>
>>>> r.
>>>>
>>>> On 2/2/20 1:49 AM, FaTune wrote:
>>>>> I see the node_groups in paraview, but don't see it if I use your
>>>> snipped:
>>>>>
>>>>> python postproc.py trian.vtk --all -b
>>>>>
>>>>> The file trian.vtk is in the attachment. Clearly something is wrong in
>>>> this
>>>>> mesh.
>>>>>
>>>>> On Sun, Feb 2, 2020 at 10:49 AM Robert Cimrman <cimrman3(a)ntc.zcu.cz>
>>>> wrote:
>>>>>
>>>>>> On 2/2/20 12:28 AM, FaTune wrote:
>>>>>>> In addition to the previous message. I created vtk mesh with values
>> in
>>>>>>> field "node_groups" to be 1 or 2. When I use 'vertices of group 0'
>>>> sfepy
>>>>>>> works without errors, but set this region to every single vertex in
>> the
>>>>>>> mesh, and I don't have values 0 in 'node_groups' field. When I
>> change 0
>>>>>> to
>>>>>>> 1 or 2 it raises error. Apparently sfepy just ignores 'node_groups'
>>>>>> field.
>>>>>>
>>>>>> It is possible to display the vertex and cell groups in a mesh with
>> the
>>>>>> following (or use any VTK viewer, such as paraview):
>>>>>>
>>>>>> python postproc.py meshes/3d/acoustic_wg.vtk --all -b
>>>>>>
>>>>>> Does it show your regions correctly? If the mesh and the node_groups
>> are
>>>>>> well
>>>>>> defined, what you do should work.
>>>>>>
>>>>>> If the above does not help you finding what's wrong, send here a
>> minimal
>>>>>> example that demonstrates the problem.
>>>>>>
>>>>>> r.
>>>>>>
>>>>>>> On Sun, Feb 2, 2020 at 10:16 AM <fatune(a)gmail.com> wrote:
>>>>>>>
>>>>>>>> regions = {
>>>>>>>> 'Omega' : 'all',
>>>>>>>> 'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'),
>>>>>>>> 'Gamma_Right' : ('vertices in (x > 99.099999)', 'facet'),
>>>>>>>> 'GammaIn': ('vertices of group 0', 'edge'),
>>>>>>>> }
>>>>>>>>
>>>>>>>>
>>>>>>>> The group I am struggling with is GammaIn. I was using
>>>>>> vibro_acoustic3d.py
>>>>>>>> as an example when I was creating my vtk mesh. Am I right in my
>>>>>> assumption
>>>>>>>> that it is enough to add field "node_groups" to my vtk and sfepy
>> will
>>>>>>>> gather information of the group number from this field?
I was thinking about meshio too. But because it does not write the old VTK
format, you could try the following:
```
import numpy as np
import meshio
from sfepy.discrete.fem import Mesh
mmesh = meshio.read('trian.vtk')
conn = mmesh.cells['tetra']
smesh = Mesh.from_data(
'meshio-mesh',
mmesh.points,
mmesh.point_data['node_groups'],
[conn],
[np.zeros_like(conn[:, 0])],
['3_4'],
)
smesh.write('trian2.vtk')
```
Then
postproc.py --only-names=node_groups -b trian2.vtk --wire
seems to show the regions correctly.
r.
On 2/2/20 1:14 PM, FaTune wrote:
> Thank you for help. I'm not sure I know how to convert the mesh into older
> format. Is there any converter? I've tried to convert trian.vtk to
> trian.mesh using meshio-convert in ubuntu. But the resulting trian.mesh
> doesn't have any information about node_groups.
>
> On Sun, Feb 2, 2020 at 9:05 PM Robert Cimrman <cimrman3(a)ntc.zcu.cz> wrote:
>
>> Can you try converting the mesh to "# vtk DataFile Version 2.0" format?
>> Your
>> mesh is in "# vtk DataFile Version 4.2", and the reader in sfepy does not
>> read
>> it correctly.
>>
>> r.
>>
>> On 2/2/20 1:49 AM, FaTune wrote:
>>> I see the node_groups in paraview, but don't see it if I use your
>> snipped:
>>>
>>> python postproc.py trian.vtk --all -b
>>>
>>> The file trian.vtk is in the attachment. Clearly something is wrong in
>> this
>>> mesh.
>>>
>>> On Sun, Feb 2, 2020 at 10:49 AM Robert Cimrman <cimrman3(a)ntc.zcu.cz>
>> wrote:
>>>
>>>> On 2/2/20 12:28 AM, FaTune wrote:
>>>>> In addition to the previous message. I created vtk mesh with values in
>>>>> field "node_groups" to be 1 or 2. When I use 'vertices of group 0'
>> sfepy
>>>>> works without errors, but set this region to every single vertex in the
>>>>> mesh, and I don't have values 0 in 'node_groups' field. When I change 0
>>>> to
>>>>> 1 or 2 it raises error. Apparently sfepy just ignores 'node_groups'
>>>> field.
>>>>
>>>> It is possible to display the vertex and cell groups in a mesh with the
>>>> following (or use any VTK viewer, such as paraview):
>>>>
>>>> python postproc.py meshes/3d/acoustic_wg.vtk --all -b
>>>>
>>>> Does it show your regions correctly? If the mesh and the node_groups are
>>>> well
>>>> defined, what you do should work.
>>>>
>>>> If the above does not help you finding what's wrong, send here a minimal
>>>> example that demonstrates the problem.
>>>>
>>>> r.
>>>>
>>>>> On Sun, Feb 2, 2020 at 10:16 AM <fatune(a)gmail.com> wrote:
>>>>>
>>>>>> regions = {
>>>>>> 'Omega' : 'all',
>>>>>> 'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'),
>>>>>> 'Gamma_Right' : ('vertices in (x > 99.099999)', 'facet'),
>>>>>> 'GammaIn': ('vertices of group 0', 'edge'),
>>>>>> }
>>>>>>
>>>>>>
>>>>>> The group I am struggling with is GammaIn. I was using
>>>> vibro_acoustic3d.py
>>>>>> as an example when I was creating my vtk mesh. Am I right in my
>>>> assumption
>>>>>> that it is enough to add field "node_groups" to my vtk and sfepy will
>>>>>> gather information of the group number from this field?
>>>>>> _______________________________________________
>>>> _______________________________________________
>>>> SfePy mailing list -- sfepy(a)python.org
>>>> To unsubscribe send an email to sfepy-leave(a)python.org
>>>> https://mail.python.org/mailman3/lists/sfepy.python.org/
>>>>
>>>
>> _______________________________________________
>> SfePy mailing list -- sfepy(a)python.org
>> To unsubscribe send an email to sfepy-leave(a)python.org
>> https://mail.python.org/mailman3/lists/sfepy.python.org/
>>
>
Can you try converting the mesh to "# vtk DataFile Version 2.0" format? Your
mesh is in "# vtk DataFile Version 4.2", and the reader in sfepy does not read
it correctly.
r.
On 2/2/20 1:49 AM, FaTune wrote:
> I see the node_groups in paraview, but don't see it if I use your snipped:
>
> python postproc.py trian.vtk --all -b
>
> The file trian.vtk is in the attachment. Clearly something is wrong in this
> mesh.
>
> On Sun, Feb 2, 2020 at 10:49 AM Robert Cimrman <cimrman3(a)ntc.zcu.cz> wrote:
>
>> On 2/2/20 12:28 AM, FaTune wrote:
>>> In addition to the previous message. I created vtk mesh with values in
>>> field "node_groups" to be 1 or 2. When I use 'vertices of group 0' sfepy
>>> works without errors, but set this region to every single vertex in the
>>> mesh, and I don't have values 0 in 'node_groups' field. When I change 0
>> to
>>> 1 or 2 it raises error. Apparently sfepy just ignores 'node_groups'
>> field.
>>
>> It is possible to display the vertex and cell groups in a mesh with the
>> following (or use any VTK viewer, such as paraview):
>>
>> python postproc.py meshes/3d/acoustic_wg.vtk --all -b
>>
>> Does it show your regions correctly? If the mesh and the node_groups are
>> well
>> defined, what you do should work.
>>
>> If the above does not help you finding what's wrong, send here a minimal
>> example that demonstrates the problem.
>>
>> r.
>>
>>> On Sun, Feb 2, 2020 at 10:16 AM <fatune(a)gmail.com> wrote:
>>>
>>>> regions = {
>>>> 'Omega' : 'all',
>>>> 'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'),
>>>> 'Gamma_Right' : ('vertices in (x > 99.099999)', 'facet'),
>>>> 'GammaIn': ('vertices of group 0', 'edge'),
>>>> }
>>>>
>>>>
>>>> The group I am struggling with is GammaIn. I was using
>> vibro_acoustic3d.py
>>>> as an example when I was creating my vtk mesh. Am I right in my
>> assumption
>>>> that it is enough to add field "node_groups" to my vtk and sfepy will
>>>> gather information of the group number from this field?
>>>> _______________________________________________
>> _______________________________________________
>> SfePy mailing list -- sfepy(a)python.org
>> To unsubscribe send an email to sfepy-leave(a)python.org
>> https://mail.python.org/mailman3/lists/sfepy.python.org/
>>
>
Hello. Is there a way to somehow mark some vertices in vtk mesh so I could later use them in region definition? I've tried to create my vtk mesh with vertices field "node_groups". And some vertices have this field to set to 1, and other to 2. But it doesnt work. Sfepy tell me
>raise ValueError('region "%s" has no entities!' % self.name)
Thank you
Hi all,
Because Python 2.7 is officially retired now, I would like to make the next sfepy release for Python 3 only. Are there any objections?
Best regards,
r.
I am pleased to announce release 2019.4 of SfePy.
Description
-----------
SfePy (simple finite elements in Python) is a software for solving systems of
coupled partial differential equations by the finite element method or by the
isogeometric analysis (limited support). It is distributed under the new BSD
license.
Home page: http://sfepy.org
Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/
Git (source) repository, issue tracker: https://github.com/sfepy/sfepy
Highlights of this release
--------------------------
- support surface terms in 1D problems
- improved Gmsh mesh format support (write .msh files)
- new updating procedure in nonlinear homogenization
- improved/faster log plotter
For full release notes see [1].
Cheers,
Robert Cimrman
[1] http://docs.sfepy.org/doc/release_notes.html#id1
---
Contributors to this release in alphabetical order:
Robert Cimrman
Vladimir Lukes
Matyas Novak
Tomáš Zítka
